This really hasn't changed much, it comes down to your play style. I, for one, still like the Dual Pistols, although I will have to give the Full Auto Rifle a try at some point. I also liked the new Pulsewave Rifle, especially against Borg who like to get close, as it gives me the most damage per shot before I have to remodulate.

Since all the weapons pretty much got balanced against each other, try finding a common version of each weapon type and experiment with how they perform, then go from there.